Multiple sequence alignment - TraesCS7A01G452700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G452700 chr7A 100.000 2604 0 0 1 2604 645335100 645337703 0.000000e+00 4809.0
1 TraesCS7A01G452700 chr2D 94.627 1489 62 14 66 1549 576453520 576454995 0.000000e+00 2290.0
2 TraesCS7A01G452700 chr2D 88.911 1479 113 35 66 1511 22573322 22574782 0.000000e+00 1775.0
3 TraesCS7A01G452700 chr2D 91.862 1069 57 13 1542 2604 576455041 576456085 0.000000e+00 1465.0
4 TraesCS7A01G452700 chr2D 84.516 465 47 12 1552 2016 357691335 357691774 1.110000e-118 436.0
5 TraesCS7A01G452700 chr2D 83.607 183 15 12 2027 2200 618378935 618379111 9.650000e-35 158.0
6 TraesCS7A01G452700 chr2D 77.239 268 43 11 2252 2503 22577806 22578071 9.720000e-30 141.0
7 TraesCS7A01G452700 chr2D 75.847 236 32 12 1007 1238 361419960 361419746 2.130000e-16 97.1
8 TraesCS7A01G452700 chr4A 88.363 1478 127 34 66 1511 705765789 705767253 0.000000e+00 1735.0
9 TraesCS7A01G452700 chr4A 80.000 245 34 14 2262 2503 69839546 69839778 1.600000e-37 167.0
10 TraesCS7A01G452700 chr4A 78.516 256 41 11 2252 2503 726657347 726657592 3.470000e-34 156.0
11 TraesCS7A01G452700 chr4A 75.465 269 48 14 2237 2503 608152984 608153236 5.890000e-22 115.0
12 TraesCS7A01G452700 chr6A 88.038 1488 120 42 66 1511 429385406 429386877 0.000000e+00 1709.0
13 TraesCS7A01G452700 chr3B 87.593 1483 117 44 66 1511 89091526 89090074 0.000000e+00 1657.0
14 TraesCS7A01G452700 chr3B 77.725 211 38 4 2252 2461 693081909 693081707 1.270000e-23 121.0
15 TraesCS7A01G452700 chr2A 88.346 1064 89 27 66 1101 174443490 174442434 0.000000e+00 1245.0
16 TraesCS7A01G452700 chr2A 81.611 658 46 26 1979 2604 710123438 710124052 2.340000e-130 475.0
17 TraesCS7A01G452700 chr2A 81.395 258 35 6 2253 2503 565166195 565165944 5.680000e-47 198.0
18 TraesCS7A01G452700 chr2A 80.676 207 24 12 443 643 610190541 610190737 2.090000e-31 147.0
19 TraesCS7A01G452700 chr2A 96.078 51 1 1 2201 2250 565164776 565164726 5.970000e-12 82.4
20 TraesCS7A01G452700 chr3D 84.946 465 46 11 1552 2016 587767533 587767973 1.420000e-122 449.0
21 TraesCS7A01G452700 chr3D 81.013 474 57 16 2038 2503 587768224 587768672 1.920000e-91 346.0
22 TraesCS7A01G452700 chr3D 80.714 280 31 10 2200 2476 477405277 477405018 2.040000e-46 196.0
23 TraesCS7A01G452700 chr5A 84.167 480 54 20 1542 2016 436072725 436072263 1.840000e-121 446.0
24 TraesCS7A01G452700 chr5A 81.600 250 32 9 2256 2503 436071579 436071342 7.350000e-46 195.0
25 TraesCS7A01G452700 chr4D 77.966 590 70 33 664 1238 386540690 386540146 5.410000e-82 315.0
26 TraesCS7A01G452700 chr4D 94.118 51 1 2 2200 2248 318747902 318747952 2.780000e-10 76.8
27 TraesCS7A01G452700 chr7D 80.714 280 31 10 2200 2476 379565311 379565052 2.040000e-46 196.0
28 TraesCS7A01G452700 chr7D 79.710 207 29 10 2251 2454 553512820 553513016 1.260000e-28 137.0
29 TraesCS7A01G452700 chr1A 84.530 181 10 13 2032 2200 466404672 466404846 2.070000e-36 163.0
30 TraesCS7A01G452700 chr1A 78.970 233 28 16 443 662 117167341 117167565 3.490000e-29 139.0
31 TraesCS7A01G452700 chr1A 87.143 70 6 3 2252 2319 117169442 117169510 2.780000e-10 76.8
32 TraesCS7A01G452700 chr5D 78.824 255 42 9 2252 2503 118852870 118852625 7.460000e-36 161.0
33 TraesCS7A01G452700 chr5D 94.118 51 1 2 2200 2248 468346020 468346070 2.780000e-10 76.8
34 TraesCS7A01G452700 chr5D 94.000 50 2 1 2200 2248 468186239 468186190 9.990000e-10 75.0
35 TraesCS7A01G452700 chr7B 86.093 151 7 7 2058 2200 4507334 4507478 1.610000e-32 150.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G452700 chr7A 645335100 645337703 2603 False 4809.0 4809 100.0000 1 2604 1 chr7A.!!$F1 2603
1 TraesCS7A01G452700 chr2D 576453520 576456085 2565 False 1877.5 2290 93.2445 66 2604 2 chr2D.!!$F4 2538
2 TraesCS7A01G452700 chr2D 22573322 22578071 4749 False 958.0 1775 83.0750 66 2503 2 chr2D.!!$F3 2437
3 TraesCS7A01G452700 chr4A 705765789 705767253 1464 False 1735.0 1735 88.3630 66 1511 1 chr4A.!!$F3 1445
4 TraesCS7A01G452700 chr6A 429385406 429386877 1471 False 1709.0 1709 88.0380 66 1511 1 chr6A.!!$F1 1445
5 TraesCS7A01G452700 chr3B 89090074 89091526 1452 True 1657.0 1657 87.5930 66 1511 1 chr3B.!!$R1 1445
6 TraesCS7A01G452700 chr2A 174442434 174443490 1056 True 1245.0 1245 88.3460 66 1101 1 chr2A.!!$R1 1035
7 TraesCS7A01G452700 chr2A 710123438 710124052 614 False 475.0 475 81.6110 1979 2604 1 chr2A.!!$F2 625
8 TraesCS7A01G452700 chr3D 587767533 587768672 1139 False 397.5 449 82.9795 1552 2503 2 chr3D.!!$F1 951
9 TraesCS7A01G452700 chr5A 436071342 436072725 1383 True 320.5 446 82.8835 1542 2503 2 chr5A.!!$R1 961
10 TraesCS7A01G452700 chr4D 386540146 386540690 544 True 315.0 315 77.9660 664 1238 1 chr4D.!!$R1 574

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
92 93 0.739813 GGTGTGGCGGATGTGAGTAC 60.740 60.0 0.00 0.0 0.0 2.73 F
1000 1050 1.583556 ATGTGGCACAGGAGATGGTA 58.416 50.0 26.04 0.0 41.8 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1549 0.034756 CCCCTTGTGACACATGACGA 59.965 55.0 20.02 0.24 0.0 4.2 R
2352 4856 0.039074 CGCTCTTTCTCGACACCACT 60.039 55.0 0.00 0.00 0.0 4.0 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.022163 GTACCTGAGTACTAGTTTGAAGCA 57.978 41.667 0.00 0.00 44.65 3.91
27 28 5.140747 ACCTGAGTACTAGTTTGAAGCAG 57.859 43.478 0.00 1.18 0.00 4.24
28 29 4.833380 ACCTGAGTACTAGTTTGAAGCAGA 59.167 41.667 0.00 0.00 0.00 4.26
29 30 5.047660 ACCTGAGTACTAGTTTGAAGCAGAG 60.048 44.000 0.00 0.00 0.00 3.35
30 31 5.184096 CCTGAGTACTAGTTTGAAGCAGAGA 59.816 44.000 0.00 0.00 0.00 3.10
31 32 6.294787 CCTGAGTACTAGTTTGAAGCAGAGAA 60.295 42.308 0.00 0.00 0.00 2.87
32 33 7.233389 TGAGTACTAGTTTGAAGCAGAGAAT 57.767 36.000 0.00 0.00 0.00 2.40
33 34 7.671302 TGAGTACTAGTTTGAAGCAGAGAATT 58.329 34.615 0.00 0.00 0.00 2.17
34 35 7.600375 TGAGTACTAGTTTGAAGCAGAGAATTG 59.400 37.037 0.00 0.00 0.00 2.32
35 36 5.619625 ACTAGTTTGAAGCAGAGAATTGC 57.380 39.130 0.00 0.00 44.41 3.56
46 47 5.573337 GCAGAGAATTGCTTCCATAGTTT 57.427 39.130 0.00 0.00 40.89 2.66
47 48 6.683974 GCAGAGAATTGCTTCCATAGTTTA 57.316 37.500 0.00 0.00 40.89 2.01
48 49 7.269477 GCAGAGAATTGCTTCCATAGTTTAT 57.731 36.000 0.00 0.00 40.89 1.40
49 50 8.383318 GCAGAGAATTGCTTCCATAGTTTATA 57.617 34.615 0.00 0.00 40.89 0.98
50 51 8.286097 GCAGAGAATTGCTTCCATAGTTTATAC 58.714 37.037 0.00 0.00 40.89 1.47
51 52 9.553064 CAGAGAATTGCTTCCATAGTTTATACT 57.447 33.333 0.00 0.00 33.66 2.12
92 93 0.739813 GGTGTGGCGGATGTGAGTAC 60.740 60.000 0.00 0.00 0.00 2.73
98 99 1.670674 GGCGGATGTGAGTACGAAACA 60.671 52.381 0.00 1.62 0.00 2.83
295 303 1.841277 AGTAGGGTTGTCAACACCACA 59.159 47.619 17.19 6.43 34.56 4.17
336 346 9.263446 TGTAGGTAGTAGGTTTTATCAACATCT 57.737 33.333 0.00 0.00 0.00 2.90
418 437 4.935352 AGAGATGATGTGTTAGGCTCTC 57.065 45.455 0.00 0.00 0.00 3.20
434 454 4.714308 AGGCTCTCTTTGCTAATCAGTAGT 59.286 41.667 0.00 0.00 31.78 2.73
577 600 9.853921 CATGTTTTTCTGAAACTTTTTCTATGC 57.146 29.630 1.58 0.00 0.00 3.14
874 918 3.511699 GCGACGCCAATGATATCTCATA 58.488 45.455 9.14 0.00 41.34 2.15
909 954 9.183368 GAAATCTTTCTCTTTGGAAGGATACAT 57.817 33.333 0.00 0.00 39.82 2.29
1000 1050 1.583556 ATGTGGCACAGGAGATGGTA 58.416 50.000 26.04 0.00 41.80 3.25
1260 1327 6.183360 GGGCGTTTATGTCATGTGTATTAACA 60.183 38.462 0.00 0.00 0.00 2.41
1301 1372 8.806146 ACTGATATTTTAGGTTGTTGCATCTTT 58.194 29.630 0.00 0.00 0.00 2.52
1429 1505 6.354039 GAAAGAGTTCGTTTCAACAACCTA 57.646 37.500 0.00 0.00 34.58 3.08
1442 1518 6.620877 TCAACAACCTAACAGGAGATACAT 57.379 37.500 0.00 0.00 37.67 2.29
1473 1549 5.806654 AAGGCAAACAAAAGGACATACAT 57.193 34.783 0.00 0.00 0.00 2.29
1479 1555 6.611381 CAAACAAAAGGACATACATCGTCAT 58.389 36.000 0.00 0.00 34.97 3.06
1540 2360 1.348036 CAAGAAGGGGAAGGACTTCGT 59.652 52.381 6.02 0.00 45.83 3.85
1550 2422 4.382793 GGGAAGGACTTCGTAGCATAACTT 60.383 45.833 6.02 0.00 40.37 2.66
1737 2618 9.209175 GTTATGTGTTTATGTTTTAATGCCCAA 57.791 29.630 0.00 0.00 0.00 4.12
1773 2657 5.722021 ATGCTTTTCGTGGGAAAACTATT 57.278 34.783 0.00 0.00 44.86 1.73
1833 2725 3.091545 TCTTTCCCCAATGATGAAGCAC 58.908 45.455 0.00 0.00 0.00 4.40
1842 2734 6.268387 CCCCAATGATGAAGCACCTATATTTT 59.732 38.462 0.00 0.00 0.00 1.82
1993 2898 7.984391 ACGAAAATAACAATGCATATCTGTGA 58.016 30.769 0.00 0.00 0.00 3.58
2290 4786 1.031235 CATGTCCCACAACAAGCACA 58.969 50.000 0.00 0.00 31.81 4.57
2328 4832 1.151899 TTGGTCACAGCTAGGGGGT 60.152 57.895 0.00 0.00 0.00 4.95
2352 4856 1.213430 ACCTTTGTTTTGTCGGAGGGA 59.787 47.619 0.00 0.00 0.00 4.20
2506 5045 1.000396 GAGGGGCCAGTTGCAATCT 60.000 57.895 4.39 0.00 43.89 2.40
2560 5100 2.721425 TTGTTTTTGTCGGAGAGGGT 57.279 45.000 0.00 0.00 36.95 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.022163 TGCTTCAAACTAGTACTCAGGTAC 57.978 41.667 0.00 0.00 46.18 3.34
4 5 6.008331 TCTGCTTCAAACTAGTACTCAGGTA 58.992 40.000 0.00 0.00 0.00 3.08
6 7 5.184096 TCTCTGCTTCAAACTAGTACTCAGG 59.816 44.000 0.00 0.00 0.00 3.86
7 8 6.260870 TCTCTGCTTCAAACTAGTACTCAG 57.739 41.667 0.00 0.00 0.00 3.35
8 9 6.650427 TTCTCTGCTTCAAACTAGTACTCA 57.350 37.500 0.00 0.00 0.00 3.41
9 10 7.412455 GCAATTCTCTGCTTCAAACTAGTACTC 60.412 40.741 0.00 0.00 39.34 2.59
10 11 6.370166 GCAATTCTCTGCTTCAAACTAGTACT 59.630 38.462 0.00 0.00 39.34 2.73
11 12 6.538444 GCAATTCTCTGCTTCAAACTAGTAC 58.462 40.000 0.00 0.00 39.34 2.73
12 13 6.727824 GCAATTCTCTGCTTCAAACTAGTA 57.272 37.500 0.00 0.00 39.34 1.82
13 14 5.619625 GCAATTCTCTGCTTCAAACTAGT 57.380 39.130 0.00 0.00 39.34 2.57
24 25 5.573337 AAACTATGGAAGCAATTCTCTGC 57.427 39.130 0.00 0.00 42.97 4.26
25 26 9.553064 AGTATAAACTATGGAAGCAATTCTCTG 57.447 33.333 0.00 0.00 32.84 3.35
53 54 4.747108 CACCGACATTGCAAACCATAAAAA 59.253 37.500 1.71 0.00 0.00 1.94
54 55 4.202161 ACACCGACATTGCAAACCATAAAA 60.202 37.500 1.71 0.00 0.00 1.52
55 56 3.319405 ACACCGACATTGCAAACCATAAA 59.681 39.130 1.71 0.00 0.00 1.40
56 57 2.887783 ACACCGACATTGCAAACCATAA 59.112 40.909 1.71 0.00 0.00 1.90
57 58 2.227626 CACACCGACATTGCAAACCATA 59.772 45.455 1.71 0.00 0.00 2.74
58 59 1.000385 CACACCGACATTGCAAACCAT 60.000 47.619 1.71 0.00 0.00 3.55
59 60 0.383590 CACACCGACATTGCAAACCA 59.616 50.000 1.71 0.00 0.00 3.67
60 61 0.318614 CCACACCGACATTGCAAACC 60.319 55.000 1.71 0.00 0.00 3.27
61 62 0.939106 GCCACACCGACATTGCAAAC 60.939 55.000 1.71 0.00 0.00 2.93
62 63 1.361993 GCCACACCGACATTGCAAA 59.638 52.632 1.71 0.00 0.00 3.68
63 64 2.902419 CGCCACACCGACATTGCAA 61.902 57.895 0.00 0.00 0.00 4.08
64 65 3.353029 CGCCACACCGACATTGCA 61.353 61.111 0.00 0.00 0.00 4.08
227 234 3.260380 CACTTCATCTCAGTCTCTTGGGT 59.740 47.826 0.00 0.00 0.00 4.51
284 292 5.858581 GCATAAAGAAGAATGTGGTGTTGAC 59.141 40.000 0.00 0.00 0.00 3.18
365 380 4.261825 CCACGGATGTACAAAAATGGTGTT 60.262 41.667 0.00 0.00 0.00 3.32
371 386 3.504520 GTCACCCACGGATGTACAAAAAT 59.495 43.478 0.00 0.00 0.00 1.82
839 881 1.354337 CGTCGCCACTGATGACCAAG 61.354 60.000 0.00 0.00 0.00 3.61
874 918 9.672673 TCCAAAGAGAAAGATTTCGAGATAATT 57.327 29.630 0.00 0.00 41.92 1.40
1000 1050 1.615392 GGGCTCAAACAAACTCTGCAT 59.385 47.619 0.00 0.00 0.00 3.96
1049 1099 4.009675 TCCTTCCAAACATACATGCTCAC 58.990 43.478 0.00 0.00 0.00 3.51
1330 1401 7.816945 AACGATCATCAAAATTGCCTAAAAG 57.183 32.000 0.00 0.00 0.00 2.27
1424 1500 7.259088 ACTTCAATGTATCTCCTGTTAGGTT 57.741 36.000 0.00 0.00 36.53 3.50
1429 1505 7.121315 GCCTTAAACTTCAATGTATCTCCTGTT 59.879 37.037 0.00 0.00 0.00 3.16
1442 1518 6.592220 GTCCTTTTGTTTGCCTTAAACTTCAA 59.408 34.615 0.00 0.00 46.96 2.69
1473 1549 0.034756 CCCCTTGTGACACATGACGA 59.965 55.000 20.02 0.24 0.00 4.20
1479 1555 2.055689 CTCTGGCCCCTTGTGACACA 62.056 60.000 3.56 3.56 0.00 3.72
1516 2336 1.202940 AGTCCTTCCCCTTCTTGTTGC 60.203 52.381 0.00 0.00 0.00 4.17
1527 2347 3.132467 AGTTATGCTACGAAGTCCTTCCC 59.868 47.826 1.61 0.00 43.93 3.97
1550 2422 1.875514 GAGCAAGACATCAACACTGCA 59.124 47.619 0.00 0.00 0.00 4.41
1553 2425 1.609061 CCCGAGCAAGACATCAACACT 60.609 52.381 0.00 0.00 0.00 3.55
1737 2618 7.754924 CCACGAAAAGCATAACAAAACATAGAT 59.245 33.333 0.00 0.00 0.00 1.98
1805 2689 7.499200 TTCATCATTGGGGAAAGAATGAAAT 57.501 32.000 0.00 0.00 40.91 2.17
1809 2693 4.160814 TGCTTCATCATTGGGGAAAGAATG 59.839 41.667 0.00 0.00 0.00 2.67
1810 2694 4.161001 GTGCTTCATCATTGGGGAAAGAAT 59.839 41.667 0.00 0.00 0.00 2.40
1811 2695 3.511146 GTGCTTCATCATTGGGGAAAGAA 59.489 43.478 0.00 0.00 0.00 2.52
2170 3365 7.643123 TCTCTCCTTTAATATGCTCCCTTTTT 58.357 34.615 0.00 0.00 0.00 1.94
2290 4786 4.516698 CCAAGTTAGAAGACATGCAGTTGT 59.483 41.667 0.00 0.00 0.00 3.32
2328 4832 1.064611 TCCGACAAAACAAAGGTCCCA 60.065 47.619 0.00 0.00 0.00 4.37
2352 4856 0.039074 CGCTCTTTCTCGACACCACT 60.039 55.000 0.00 0.00 0.00 4.00
2506 5045 5.303165 TGTGACTAAGTTAGAGAGACGTGA 58.697 41.667 16.89 0.00 0.00 4.35
2560 5100 2.121538 CCCATCTCTCTCGACGCCA 61.122 63.158 0.00 0.00 0.00 5.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.